Mercurial > repos > iuc > pygenometracks

annotate pyGenomeTracks.xml @ 12:14e7c35f3d00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
author iuc
date Wed, 25 Jan 2023 15:33:12 +0000
parents 7dd841a32245
children 360df4999907
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a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
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1 <tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>plot genomic data tracks</description>
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3 <macros>
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4 <token name="@BINARY@">pyGenomeTracks</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 ## First symlink data
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11 ## of hic to have the good extension
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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12 ## of fasta to have the index written in the working directory
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c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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13 #for $counter, $track in enumerate($tracks):
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7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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14 #if $track.track_file_style_conditional.track_file_style_selector in ["hic_matrix_option", "hic_matrix_square_option"]:
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15 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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16 #set ext = $data_matrix.extension
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17 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
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18 #end for
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19 #end if
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20 #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option":
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21 #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history":
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22 ln -s $track.track_file_style_conditional.fasta_source.fasta_local fasta_${counter}.fa &&
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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23 #end if
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24 #end if
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25 #end for
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26
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28 sed '/^$/d' '$tracks_config' &&
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29 @BINARY@
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30 --tracks '$tracks_config'
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31 --region '$region'
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32 #if $global_args.title != '':
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33 --title '$global_args.title'
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34 #end if
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35 #if $global_args.plotWidth != '':
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36 --plotWidth $global_args.plotWidth
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37 #else:
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38 --width $global_args.width
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39 #end if
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40 #if $global_args.height != '':
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41 --height '$global_args.height'
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42 #end if
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43 --fontSize $global_args.fontsize
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44 --dpi $global_args.dpi
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45 --trackLabelFraction $global_args.trackLabelFraction
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46 --trackLabelHAlign $global_args.trackLabelHAlign
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47 --outFileName plot.$image_file_format
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48 $global_args.decreasingXAxis
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49 && mv plot.$image_file_format plot
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50 ]]>
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51 </command>
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52 <configfiles>
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53 <configfile name="tracks_config">
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54 ## Each track:
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55 #for $counter, $track in enumerate($tracks):
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56 ## Hi-C Track triangle
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57 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
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58 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
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59 [hic_section_${counter}_${counter_matrix}]
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60 #set ext = $data_matrix.extension
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61 file = ${counter}_${counter_matrix}.$ext
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62 file_type = hic_matrix
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63 #if $track.track_file_style_conditional.title:
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64 title = $track.track_file_style_conditional.title
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65 #else:
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66 title = $data_matrix.element_identifier
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67 #end if
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68 #if $track.track_file_style_conditional.depth:
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69 depth = $track.track_file_style_conditional.depth
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70 #end if
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71 #if $track.track_file_style_conditional.colormap:
0
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72 colormap = $track.track_file_style_conditional.colormap
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73 #end if
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74 #if $track.track_file_style_conditional.min_value != "":
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75 min_value = $track.track_file_style_conditional.min_value
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76 #end if
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77 #if $track.track_file_style_conditional.max_value != "":
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78 max_value = $track.track_file_style_conditional.max_value
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79 #end if
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80 transform = $track.track_file_style_conditional.transform
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81 #if $track.track_file_style_conditional.height_matrix != "":
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82 height = $track.track_file_style_conditional.height_matrix
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83 #end if
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84 #if $track.track_file_style_conditional.show_masked_bins:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
85 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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86 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
87 #if $track.track_file_style_conditional.invert_orientation:
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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88 orientation = inverted
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
89 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
90 #if $track.track_file_style_conditional.scale_factor:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
91 scale_factor = $track.track_file_style_conditional.scale_factor
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
92 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
93 rasterize = $track.track_file_style_conditional.rasterize
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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94 ## If a boundary file is given a new section needs to be written:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
95 #if str($track.track_file_style_conditional.boundaries_file) != "None":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
96 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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97 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
98 #else:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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99 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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100 #end if
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
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101 [tads_${counter}_${counter_matrix}]
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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102 file = $boundary_file
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
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103 file_type = domains
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
104 border_color = black
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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105 color = none
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
106 overlay_previous = share-y
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
107 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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108 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
109 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
110 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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diff changeset
111 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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112 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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diff changeset
113 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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114 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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diff changeset
115
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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116 ## Hi-C Track square
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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117 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_square_option":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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118 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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119 [hic_section_${counter}_${counter_matrix}]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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120 #set ext = $data_matrix.extension
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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121 file = ${counter}_${counter_matrix}.$ext
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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122 file_type = hic_matrix_square
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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123 #if $track.track_file_style_conditional.title:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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124 title = $track.track_file_style_conditional.title
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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125 #else:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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126 title = $data_matrix.element_identifier
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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127 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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128 #if $track.track_file_style_conditional.region2:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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129 region2 = $track.track_file_style_conditional.region2
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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130 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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131 #if $track.track_file_style_conditional.colormap:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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132 colormap = $track.track_file_style_conditional.colormap
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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133 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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134 #if $track.track_file_style_conditional.min_value != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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135 min_value = $track.track_file_style_conditional.min_value
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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136 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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137 #if $track.track_file_style_conditional.max_value != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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138 max_value = $track.track_file_style_conditional.max_value
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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139 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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140 transform = $track.track_file_style_conditional.transform
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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141 #if $track.track_file_style_conditional.height_matrix != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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142 height = $track.track_file_style_conditional.height_matrix
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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143 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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144 #if $track.track_file_style_conditional.show_masked_bins:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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145 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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146 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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147 #if $track.track_file_style_conditional.invert_orientation:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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148 orientation = inverted
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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149 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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150 #if $track.track_file_style_conditional.scale_factor:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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151 scale_factor = $track.track_file_style_conditional.scale_factor
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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diff changeset
152 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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153 rasterize = $track.track_file_style_conditional.rasterize
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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154 ## If a boundary file is given a new section needs to be written:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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155 #if str($track.track_file_style_conditional.boundaries_file) != "None":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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156 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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157 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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diff changeset
158 #else:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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159 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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diff changeset
160 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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161 [tads_${counter}_${counter_matrix}]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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162 file = $boundary_file
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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163 file_type = bed
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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164 display = squares
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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165 border_color = black
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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166 color = none
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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diff changeset
167 overlay_previous = share-y
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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diff changeset
168 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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169 ## If spacer is asked a new section is created:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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170 #if $track.track_file_style_conditional.spacer_height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
171 [spacer]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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172 height = $track.track_file_style_conditional.spacer_height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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diff changeset
173 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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174 #end for
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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175 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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176
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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177 ## Chrom_state track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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178 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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179 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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180 [chrom states_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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181 file = $data_bed
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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182 #if $track.track_file_style_conditional.title:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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183 title = $track.track_file_style_conditional.title
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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184 #else:
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
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185 title = $data_bed.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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186 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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187 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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188 color = bed_rgb
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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189 #elif $track.track_file_style_conditional.color_bed.color:
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
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190 color = $track.track_file_style_conditional.color_bed.color
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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191 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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192 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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193 border_color = $track.track_file_style_conditional.border_color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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194 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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195 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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196 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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197 display = collapsed
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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198 #if $track.track_file_style_conditional.height_chrom:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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199 height = $track.track_file_style_conditional.height_chrom
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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200 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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201 line_width = $track.track_file_style_conditional.line_width
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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202 file_type = bed
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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203 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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204 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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205 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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206 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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207 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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208 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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209 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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210
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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211 ## Gene/gtf track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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212 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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213 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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214 [genes_${counter}_${counter_bed}]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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215 #set ext = $data_bed.extension
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
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216 file = $data_bed
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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217 #if $ext == 'gtf':
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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218 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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219 #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true':
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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220 merge_transcripts = true
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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221 merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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222 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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223 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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224 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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225 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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226 #elif $track.track_file_style_conditional.overlay_select == 'no':
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
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227 title = $data_bed.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
228 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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parents: 4
diff changeset
229 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
230 color = bed_rgb
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
231 #elif $track.track_file_style_conditional.color_bed.color:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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232 color = $track.track_file_style_conditional.color_bed.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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233 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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234 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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diff changeset
235 border_color = $track.track_file_style_conditional.border_color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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236 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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237 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
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diff changeset
238 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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239 style = $track.track_file_style_conditional.bed_style.bed_style_select
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
240 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
241 arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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242 #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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243 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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diff changeset
244 #else
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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245 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
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246 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
247 #else:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
248 height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
249 #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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diff changeset
250 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
251 #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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diff changeset
252 color_utr = bed_rgb
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
253 #else:
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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254 ## This is 'like'
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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diff changeset
255 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
256 color_utr = bed_rgb
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
257 #else:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
258 color_utr = $track.track_file_style_conditional.color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
259 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
260 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
261 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
262 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
263 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
264 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
265 arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
266 arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
267 #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
268 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
269 #else
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
270 color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
271 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
272 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
273 #end if
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
274 display = $track.track_file_style_conditional.display
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
275 #if $track.track_file_style_conditional.height_bed:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
276 height = $track.track_file_style_conditional.height_bed
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
277 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
278 labels = $track.track_file_style_conditional.labels.plot_labels
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
279 #if $track.track_file_style_conditional.labels.plot_labels == 'true':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
280 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
281 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
282 fontstyle = $track.track_file_style_conditional.labels.fontstyle
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
283 #if $track.track_file_style_conditional.labels.fontsize:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
284 fontsize = $track.track_file_style_conditional.labels.fontsize
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
285 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
286 #end if
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
287 file_type = $ext
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
288 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
289 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
290 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
291 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
292 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
293 line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
294 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
295 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
296 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
297 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
298 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
299 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
300 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
301 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
302 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
303 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
304 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
305
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
306 ## Link
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
307 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
308 [links_$counter]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
309 file = $track.track_file_style_conditional.track_input_link
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
310 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
311 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
312 #elif $track.track_file_style_conditional.overlay_select == 'no':
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
313 title = $track.track_file_style_conditional.track_input_link.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
314 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
315 #if $track.track_file_style_conditional.height:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
316 height = $track.track_file_style_conditional.height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
317 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
318 #if $track.track_file_style_conditional.min_value != "":
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
319 min_value = $track.track_file_style_conditional.min_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
320 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
321 #if $track.track_file_style_conditional.max_value != "":
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
322 max_value = $track.track_file_style_conditional.max_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
323 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
324 color = $track.track_file_style_conditional.color_link.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
325 alpha = $track.track_file_style_conditional.alpha
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
326 line_width = $track.track_file_style_conditional.line_width
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
327 line_style = $track.track_file_style_conditional.line_style
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
328 links_type = $track.track_file_style_conditional.display.links_type
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
329 #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
330 compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
331 use_middle = $track.track_file_style_conditional.display.use_middle
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
332 #end if
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
333 #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
334 ylim = $track.track_file_style_conditional.display.ylim
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
335 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
336 #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
337 region2 = $track.track_file_style_conditional.display.region2
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
338 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
339 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
340 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
341 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
342 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
343 file_type = links
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
344 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
345 #if $track.track_file_style_conditional.spacer_height != "":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
346 [spacer]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
347 height = $track.track_file_style_conditional.spacer_height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
348 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
349 #end if
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
350
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
351 ## Narrow peak
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
352 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
353 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
354 [narrow_peak_${counter}_${counter_narrow_peak}]
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
355 file = $data_narrow_peak
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
356 #if $track.track_file_style_conditional.title:
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
357 title = $track.track_file_style_conditional.title
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
358 #elif $track.track_file_style_conditional.overlay_select == 'no':
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
359 title = $data_narrow_peak.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
360 #end if
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
361 color = $track.track_file_style_conditional.color
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
362 type = $track.track_file_style_conditional.display.display_selector
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
363 use_summit = $track.track_file_style_conditional.display.use_summit
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
364 #if $track.track_file_style_conditional.display.display_selector == "peak":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
365 show_data_range = $track.track_file_style_conditional.display.show_data
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
366 #if $track.track_file_style_conditional.display.width_adjust:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
367 width_adjust = $track.track_file_style_conditional.display.width_adjust
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
368 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
369 #if $track.track_file_style_conditional.display.min_value != "":
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
370 min_value = $track.track_file_style_conditional.display.min_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
371 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
372 #if $track.track_file_style_conditional.display.max_value != "":
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
373 max_value = $track.track_file_style_conditional.display.max_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
374 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
375 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
376 #if $track.track_file_style_conditional.height_narrow_peak:
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
377 height = $track.track_file_style_conditional.height_narrow_peak
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
378 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
379 line_width = $track.track_file_style_conditional.line_width
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
380 file_type = narrow_peak
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
381 show_labels = $track.track_file_style_conditional.labels.show_labels
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
382 #if $track.track_file_style_conditional.labels.show_labels == 'true':
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
383 #if $track.track_file_style_conditional.labels.fontsize:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
384 fontsize = $track.track_file_style_conditional.labels.fontsize
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
385 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
386 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
387 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
388 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
389 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
390 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
391 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
392 #if $track.track_file_style_conditional.spacer_height != "":
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
393 [spacer]
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
394 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
395 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
396 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
397 #end if
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
398
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
399 ## Bedgraph track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
400 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
401 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
402 [bedgraph_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
403 file = $data_bedgraph
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
404 #if $track.track_file_style_conditional.title:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
405 title = $track.track_file_style_conditional.title
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
406 #elif $track.track_file_style_conditional.overlay_select == "no":
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
407 title = $data_bedgraph.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
408 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
409 #if $track.track_file_style_conditional.color:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
410 color = $track.track_file_style_conditional.color
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
411 #end if
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
412 alpha = $track.track_file_style_conditional.alpha
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
413 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
414 negative_color = $track.track_file_style_conditional.color_negative.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
415 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
416 #if $track.track_file_style_conditional.height_bedgraph:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
417 height = $track.track_file_style_conditional.height_bedgraph
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
418 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
419 #if $track.track_file_style_conditional.min_value != "":
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
420 min_value = $track.track_file_style_conditional.min_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
421 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
422 #if $track.track_file_style_conditional.max_value != "":
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
423 max_value = $track.track_file_style_conditional.max_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
424 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
425 show_data_range = $track.track_file_style_conditional.show_data
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
426 grid = $track.track_file_style_conditional.grid
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
427 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
428 use_middle = $track.track_file_style_conditional.use_middle
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
429 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
430 #if $columns > 4:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
431 file_type = bedgraph_matrix
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
432 type = lines
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
433 #else:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
434 file_type = bedgraph
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
435 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
436 type = fill
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
437 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
438 type = line:$track.track_file_style_conditional.type_conditional.width_line
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
439 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
440 type = points:$track.track_file_style_conditional.type_conditional.width_point
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
441 #end if
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
442 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
443 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
444 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
445 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
446 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
447 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
448 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
449 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
450 #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
451 summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
452 #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
453 number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
454 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
455 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
456 #if $track.track_file_style_conditional.op.operation != 'file':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
457 operation = $track.track_file_style_conditional.op.operation
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
458 #if 'second_file' in str($track.track_file_style_conditional.op.operation):
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
459 second_file = $track.track_file_style_conditional.op.second_file
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
460 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
461 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
462 #if $track.track_file_style_conditional.invert_orientation:
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
463 orientation = inverted
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
464 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
465 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
466 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
467 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
468 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
469 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
470 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
471 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
472 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
473
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
474 ## Bigwig tracks
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
475 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
476 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
477 [bigwig_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
478 file = $data_bigwig
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
479 #if $track.track_file_style_conditional.title:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
480 title = $track.track_file_style_conditional.title
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
481 #elif $track.track_file_style_conditional.overlay_select == "no":
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
482 title = $data_bigwig.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
483 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
484 #if $track.track_file_style_conditional.color:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
485 color = $track.track_file_style_conditional.color
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
486 #end if
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
487 alpha = $track.track_file_style_conditional.alpha
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
488 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
489 negative_color = $track.track_file_style_conditional.color_negative.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
490 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
491 #if $track.track_file_style_conditional.min_value != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
492 min_value = $track.track_file_style_conditional.min_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
493 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
494 #if $track.track_file_style_conditional.max_value != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
495 max_value = $track.track_file_style_conditional.max_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
496 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
497 height = $track.track_file_style_conditional.height_bigwig
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
498 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
499 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
500 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
501 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
502 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
503 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
504 type = fill
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
505 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
506 type = line:$track.track_file_style_conditional.type_conditional.width_line
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
507 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
508 type = points:$track.track_file_style_conditional.type_conditional.width_point
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
509 #end if
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
510 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
511 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
512 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
513 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
514 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
515 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
516 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
517 #if $track.track_file_style_conditional.op.operation != 'file':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
518 operation = $track.track_file_style_conditional.op.operation
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
519 #if 'second_file' in $track.track_file_style_conditional.op.operation:
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
520 second_file = $track.track_file_style_conditional.op.second_file
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
521 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
522 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
523 show_data_range = $track.track_file_style_conditional.show_data
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
524 grid = $track.track_file_style_conditional.grid
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
525 file_type = bigwig
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
526 #if $track.track_file_style_conditional.invert_orientation:
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
527 orientation = inverted
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
528 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
529 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
530 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
531 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
532 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
533 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
534 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
535 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
536 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
537
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
538 ## bedgraph_matrix
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
539 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
540 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
541 [bedgraph_matrix_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
542 file = $data_bedgraph_matrix
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
543 #if $track.track_file_style_conditional.title:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
544 title = $track.track_file_style_conditional.title
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
545 #else:
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
546 title = $data_bedgraph_matrix.element_identifier
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
547 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
548 #if $track.track_file_style_conditional.height_bedgraph:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
549 height = $track.track_file_style_conditional.height_bedgraph
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
550 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
551 #if $track.track_file_style_conditional.min_value != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
552 min_value = $track.track_file_style_conditional.min_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
553 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
554 #if $track.track_file_style_conditional.max_value != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
555 max_value = $track.track_file_style_conditional.max_value
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
556 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
557 type = $track.track_file_style_conditional.type.type_selector
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
558 file_type = bedgraph_matrix
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
559 #if $track.track_file_style_conditional.type.type_selector == 'lines':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
560 show_data_range = $track.track_file_style_conditional.type.show_data
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
561 plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
562 pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
563 individual_color = $track.track_file_style_conditional.type.individual_color
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
564 summary_color = $track.track_file_style_conditional.type.summary_color
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
565 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
566 colormap = $track.track_file_style_conditional.type.colormap
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
567 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
568 #if $track.track_file_style_conditional.invert_orientation:
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
569 orientation = inverted
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
570 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
571 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
572 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
573 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
574 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
575 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
576 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
577 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
578
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
579 ## Vlines:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
580 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
581 [vlines_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
582 file = $track.track_file_style_conditional.track_input_bed_single
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
583 line_width = $track.track_file_style_conditional.line_width
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
584 line_style = $track.track_file_style_conditional.line_style
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
585 color = $track.track_file_style_conditional.color
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
586 alpha = $track.track_file_style_conditional.alpha
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
587 zorder = $track.track_file_style_conditional.zorder
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
588 type = vlines
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
589 #end if
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
590
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
591 ## Vhighlight:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
592 #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
593 [vhighlight_$counter]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
594 file = $track.track_file_style_conditional.track_input_bed_single
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
595 line_width = $track.track_file_style_conditional.line_width
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
596 color = $track.track_file_style_conditional.color
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
597 alpha = $track.track_file_style_conditional.alpha
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
598 border_color = $track.track_file_style_conditional.border_color
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
599 type = vhighlight
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
600 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
601
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
602 ## Hlines:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
603 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
604 [hlines_$counter]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
605 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
606 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
607 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
608 #if $track.track_file_style_conditional.height:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
609 height = $track.track_file_style_conditional.height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
610 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
611 #if $track.track_file_style_conditional.min_value != "":
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
612 min_value = $track.track_file_style_conditional.min_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
613 #end if
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
614 #if $track.track_file_style_conditional.max_value != "":
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
615 max_value = $track.track_file_style_conditional.max_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
616 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
617 y_values = $track.track_file_style_conditional.y_values
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
618 show_data_range = $track.track_file_style_conditional.show_data
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
619 color = $track.track_file_style_conditional.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
620 alpha = $track.track_file_style_conditional.alpha
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
621 line_width = $track.track_file_style_conditional.line_width
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
622 line_style = $track.track_file_style_conditional.line_style
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
623 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
624 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
625 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
626 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
627 file_type = hlines
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
628 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
629 #if $track.track_file_style_conditional.spacer_height != "":
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
630 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
631 height = $track.track_file_style_conditional.spacer_height
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
632 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
633 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
634
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
635 ## Spacer
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
636 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
637 [spacer]
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
638 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
639 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
640 #end if
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
641 #if $track.track_file_style_conditional.spacer_height != "":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
642 height = $track.track_file_style_conditional.spacer_height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
643 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
644 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
645
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
646 ## Xaxis:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
647 #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
648 [x-axis]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
649 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
650 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
651 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
652 #if $track.track_file_style_conditional.fontsize != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
653 fontsize = $track.track_file_style_conditional.fontsize
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
654 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
655 where = $track.track_file_style_conditional.xaxis_where
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
656 ## If spacer is asked a new section is created:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
657 #if $track.track_file_style_conditional.spacer_height != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
658 [spacer]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
659 height = $track.track_file_style_conditional.spacer_height
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
660 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
661 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
662
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
663 ## Scale bar:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
664 #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
665 [scale_bar]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
666 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
667 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
668 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
669 #if $track.track_file_style_conditional.color != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
670 color = $track.track_file_style_conditional.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
671 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
672 alpha = $track.track_file_style_conditional.alpha
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
673 line_width = $track.track_file_style_conditional.line_width
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
674 #if $track.track_file_style_conditional.scalebar_pos.x_center != "":
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
675 x_center = $track.track_file_style_conditional.scalebar_pos.x_center
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
676 #end if
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
677 #if $track.track_file_style_conditional.scalebar_pos.size != "":
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
678 size = $track.track_file_style_conditional.scalebar_pos.size
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
679 #end if
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
680 #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "":
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
681 scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
682 #end if
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
683 #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "":
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
684 scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
685 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
686 where = $track.track_file_style_conditional.sb_where
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
687 #if $track.track_file_style_conditional.fontsize != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
688 fontsize = $track.track_file_style_conditional.fontsize
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
689 #end if
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
690 #if $track.track_file_style_conditional.height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
691 height = $track.track_file_style_conditional.height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
692 #end if
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
693 file_type = scalebar
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
694 ## If spacer is asked a new section is created:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
695 #if $track.track_file_style_conditional.spacer_height != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
696 [spacer]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
697 height = $track.track_file_style_conditional.spacer_height
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
698 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
699 #end if
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
700
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
701 ## Fasta:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
702 #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
703 [Fasta_${counter}]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
704 #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
705 file = fasta_${counter}.fa
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
706 #else:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
707 file = $track.track_file_style_conditional.fasta_source.fasta_cached.fields.path
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
708 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
709 #if $track.track_file_style_conditional.title:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
710 title = $track.track_file_style_conditional.title
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
711 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
712 #if $track.track_file_style_conditional.height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
713 height = $track.track_file_style_conditional.height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
714 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
715 #if $track.track_file_style_conditional.invert_orientation:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
716 orientation = inverted
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
717 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
718 overlay_previous = $track.track_file_style_conditional.overlay_select
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
719 file_type = fasta
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
720 ## If spacer is asked a new section is created:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
721 #if $track.track_file_style_conditional.spacer_height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
722 [spacer]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
723 height = $track.track_file_style_conditional.spacer_height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
724 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
725 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
726
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
727 ## Maf:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
728 #if $track.track_file_style_conditional.track_file_style_selector == "maf_option":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
729 [Maf_${counter}]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
730 file = $track.track_file_style_conditional.track_input_maf
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
731 file_index = $track.track_file_style_conditional.track_input_maf.metadata.maf_index
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
732 reference = $track.track_file_style_conditional.reference
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
733 #if $track.track_file_style_conditional.title:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
734 title = $track.track_file_style_conditional.title
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
735 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
736 #if $track.track_file_style_conditional.height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
737 height = $track.track_file_style_conditional.height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
738 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
739 #if $track.track_file_style_conditional.invert_orientation:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
740 orientation = inverted
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
741 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
742 overlay_previous = $track.track_file_style_conditional.overlay_select
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
743 line_width = $track.track_file_style_conditional.line_width
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
744 color_identical = $track.track_file_style_conditional.color_identical
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
745 color_mismatch = $track.track_file_style_conditional.color_mismatch
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
746 color_gap = $track.track_file_style_conditional.color_gap
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
747 #if $track.track_file_style_conditional.species_order != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
748 species_order = $track.track_file_style_conditional.species_order
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
749 #if $track.track_file_style_conditional.species_labels != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
750 species_labels = $track.track_file_style_conditional.species_labels
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
751 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
752 species_order_only = $track.track_file_style_conditional.species_order_only
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
753 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
754 display_ref_seq = $track.track_file_style_conditional.display_ref_seq
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
755 file_type = maf
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
756 ## If spacer is asked a new section is created:
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
757 #if $track.track_file_style_conditional.spacer_height != "":
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
758 [spacer]
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
759 height = $track.track_file_style_conditional.spacer_height
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
760 #end if
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
761 #end if
1
0ea86f6bf2a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf
iuc
parents: 0
diff changeset
762 #end for
0ea86f6bf2a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf
iuc
parents: 0
diff changeset
763 </configfile>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
764 </configfiles>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
765 <inputs>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
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parents: 6
diff changeset
766 <!--Arguments for pgt-->
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
767 <param argument="--region" type="text" label="Region of the genome to plot" optional="false"
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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parents: 8
diff changeset
768 help="The format is chr:start-end, for example chr10:10-500">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
769 <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
770 </param>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
771 <section name="global_args" title="Configure figure parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
772 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
773 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
774 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
775 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
776 <param argument="--width" type="float" label="Figure width in cm" value="40"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
777 <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true"
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
778 help="This will overwrite what has been defined as a figure width."/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
779 <param argument="--height" type="float" label="Figure height in centimeters" optional="true"
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
780 help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
781 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
782 min="0" max="1"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
783 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
784 <option value="left" selected="True">left</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
785 <option value="right">right</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
786 <option value="center">center</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
787 </param>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
788 <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
789 label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
790 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
791 <!--Info to build the config file-->
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
792 <repeat name="tracks" min="1" title="Include tracks in your plot"
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
793 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
794 The order you add them represent the order they will be plotted from top to bottom.">
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
795 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
796 <param name="track_file_style_selector" type="select" label="Choose style of the track">
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
797 <option value="hic_matrix_option">TAD visualization (triangle)</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
798 <option value="hic_matrix_square_option">TAD visualization (square)</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
799 <option value="chrom_states_option">Chromatine states</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
800 <option value="gene_track_option">Gene track / Bed track</option>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
801 <option value="link_track_option">Link track</option>
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
802 <option value="narrow_peak_track_option">NarrowPeak track</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
803 <option value="bigwig_track_option">Bigwig track</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
804 <option value="bedgraph_track_option">Bedgraph track </option>
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
805 <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
806 <option value="vlines_track_option">Vlines track</option>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
807 <option value="vhighlight_track_option">Vhighlight track</option>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
808 <option value="hlines_track_option">Hlines track</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
809 <option value="spacer_option">Spacer</option>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
810 <option value="xaxis_option">X-axis</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
811 <option value="scale_bar_option">Scale bar track</option>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
812 <option value="fasta_option">Fasta track</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
813 <option value="maf_option">Maf track</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
814 </param>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
815 <when value="hic_matrix_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
816 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
817 <expand macro="matrix_h5_cooler_multiple_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
818
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
819 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
820 <option value="RdYlBu_r">RdYlBu reversed</option>
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
821 <option value="viridis">viridis</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
822 <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
823 </param>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
824 <expand macro="minmax_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
825 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
826 <param name="transform" type="select" label="Plot the transformed value">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
827 <option value="log1p" selected="True" >log1p</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
828 <option value="log">log</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
829 <option value="-log">-log</option>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
830 <option value="no">no transformation</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
831
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
832 </param>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
833 <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares rotated 45 degrees."/>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
834 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
835 label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
836 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display triangles on top of the heatmap"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
837 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
838 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
839 label="Rasterize the heatmap" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
840 <expand macro="inverted_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
841 <expand macro="spacer_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
842
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
843 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
844
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
845 <when value="hic_matrix_square_option">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
846 <expand macro="plot_title" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
847 <expand macro="matrix_h5_cooler_multiple_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
848
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
849 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
850 <option value="RdYlBu_r">RdYlBu reversed</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
851 <option value="viridis">viridis</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
852 <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
853 </param>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
854 <expand macro="minmax_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
855 <expand macro="region2_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
856 <param name="transform" type="select" label="Plot the transformed value">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
857 <option value="log1p" selected="True" >log1p</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
858 <option value="log">log</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
859 <option value="-log">-log</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
860 <option value="no">no transformation</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
861
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
862 </param>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
863 <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares."/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
864 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
865 label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
866 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display squares on top of the heatmap"/>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
867 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
868 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
869 label="Rasterize the heatmap" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
870 <expand macro="inverted_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
871 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
872
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
873 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
874 <when value="chrom_states_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
875 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
876 <expand macro="track_input_bed_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
877 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
878 <param name="color_bed_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
879 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
880 <option value="bed_rgb">From the 9th field</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
881 <option value="colormap">From the 5th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
882 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
883 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
884 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
885 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
886 <when value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
887 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
888 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
889 <option value="RdYlBu_r">RdYlBu reversed</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
890 <option value="viridis">viridis</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
891 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
892 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
893 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
894 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
895 <expand macro="border_color_bed_macro" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
896 <param name="line_width" type="float" value="0.5" label="width of lines" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
897 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
898 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
899 label="Plot labels" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
900 <expand macro="spacer_macro" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
901
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
902 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
903 <when value="gene_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
904 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
905
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
906 <expand macro="track_input_bed_gtf_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
907 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
908 <param name="color_bed_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
909 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
910 <option value="bed_rgb">From the 9th field</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
911 <option value="colormap">From the 5th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
912 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
913 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
914 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
915 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
916 <when value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
917 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
918 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
919 <option value="RdYlBu_r">RdYlBu reversed</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
920 <option value="viridis">viridis</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
921 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
922 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
923 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
924 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
925 <expand macro="border_color_bed_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
926 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
927 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
928 <param name="plot_labels" type="select" label="Plot labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
929 <option value="true" selected="True">yes</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
930 <option value="false">no</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
931 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
932 <when value="true">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
933 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
934 label="Put all labels inside the plotted region"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
935 help="Put labels on the left of the region if the region ends after the plotted region."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
936 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
937 label="Allow to put labels in the right margin"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
938 help="Put labels in the margin if the region ends after the plotted region."/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
939 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
940 <param name="fontstyle" type="select" label="Fontstyle">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
941 <option value="normal" selected="True">normal</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
942 <option value="italic">italic</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
943 <option value="oblique">oblique</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
944 </param>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
945 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
946 <when value="false"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
947 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
948 <param name="display" type="select" label="display to use">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
949 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
950 <option value="interleaved">interleaved (everything on 2 lines)</option>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
951 <option value="collapsed">collapsed (everything on 1 line)</option>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
952 <option value="triangles">triangles (plot triangles between start and end)</option>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
953 <option value="squares">squares (plot squares on the diagonal)</option>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
954 </param>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
955 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
956 <param name="bed_style_select" type="select" label="Bed style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
957 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
958 <option value="UCSC">UCSC (blocks with arrows in introns)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
959 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
960 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
961 <when value="flybase">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
962 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
963 label="Include the arrowhead in the bed interval:"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
964 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
965 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
966 label="Size of arrowhead relative to the plotted region"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
967 help="This size is also used to put space between the bed regions and their labels."/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
968 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
969 <expand macro="utr_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
970 <expand macro="bed_advanced_macro" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
971 <expand macro="backbone_color_bed_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
972 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
973 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
974 <when value="UCSC">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
975 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
976 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
977 <expand macro="bed_advanced_macro" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
978 <expand macro="backbone_color_bed_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
979 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
980 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
981 <when value="tssarrow">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
982 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
983 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
984 <expand macro="utr_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
985 <expand macro="bed_advanced_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
986 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
987 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
988 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
989 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
990 <expand macro="inverted_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
991 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
992
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
993 </when>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
994 <when value="link_track_option">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
995 <expand macro="plot_title" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
996 <expand macro="track_input_link_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
997 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
998 <param name="color_link_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
999 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1000 <option value="colormap">From the 7th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1001 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1002 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1003 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1004 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1005 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1006 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1007 <option value="RdYlBu_r">RdYlBu reversed</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1008 <option value="viridis">viridis</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1009 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1010 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1011 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1012 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1013 <expand macro="lines_macro" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1014 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1015 <param name="links_type" type="select" label="Representation of the link:">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1016 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1017 <option value="triangles">triangles</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1018 <option value="loops">loops (a diamond highlighting the intersection)</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1019 <option value="squares">squares (a square highlighting the intersection symetrically to the diagonal)</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1020 </param>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1021 <when value="arcs">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1022 <expand macro="links_arcs_triangles_options" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1023 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1024 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1025 <when value="triangles">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1026 <expand macro="links_arcs_triangles_options" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1027 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1028 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1029 <when value="loops">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1030 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1031 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1032 <when value="squares">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1033 <expand macro="region2_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1034 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1035 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1036 <param name="height" type="float" value="1.5" optional="True" label="height"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1037 <expand macro="minmax_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1038 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1039 <expand macro="inverted_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1040 <expand macro="spacer_macro" />
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
1041 </when>
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1042 <when value="narrow_peak_track_option">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1043 <expand macro="plot_title" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1044 <expand macro="track_input_narrow_peak_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1045 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1046 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1047 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1048 <param name="display_selector" type="select" label="display to use">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1049 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1050 <option value="box">box: Draw a box</option>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1051 </param>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1052 <when value="peak">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1053 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1054 optional="True" label="Use summit information to make the curve." />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1055 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1056 label="Show visualization of data range" />
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
1057 <param name="width_adjust" type="float" value="1.5" optional="True"
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1058 label="Factor to change the width of the curve."/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1059 <expand macro="minmax_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1060 </when>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1061 <when value="box">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1062 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1063 optional="True" label="Plot a vertical bar at the summit position." />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1064 </when>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1065 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1066 <param name="line_width" type="float" value="1" label="width of lines" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1067 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1068 <param name="show_labels" type="select" label="Plot labels (name, p-val, q-val)">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1069 <option value="true" selected="True">yes</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1070 <option value="false">no</option>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1071 </param>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1072 <when value="true">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1073 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1074 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1075 <when value="false"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1076 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1077 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1078 <expand macro="inverted_macro" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1079 <expand macro="spacer_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1080
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1081 </when>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1082 <when value="bedgraph_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1083 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1084 <expand macro="track_input_bedgraph_macro" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1085 <expand macro="color_coverage_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1086 <expand macro="minmax_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1087 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1088 <expand macro="type_coverage_macro" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1089 <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1090 <param name="summary_method" type="select" label="Summary method">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1091 <option value="no" selected="True">no=no summary method (keep all values)</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1092 <option value="mean">mean=mean value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1093 <option value="min">min=minimum value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1094 <option value="max">max=maximum value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1095 <option value="coverage">coverage=number of covered bases</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1096 <option value="std">std=standard deviation</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1097 </param>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1098 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1099 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1100 <expand macro="logScale_coverage_macro" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1101 <section name ="op" title="Compute an operation on the file" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1102 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1103 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1104 <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1105 </section>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1106 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1107 label="NAN's to zeros" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1108 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1109 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1110 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1111 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1112 <expand macro="inverted_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1113 <expand macro="overlay_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1114 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1115 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1116 <when value="bigwig_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1117 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1118
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1119 <expand macro="track_input_bigwig_macro" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1120 <expand macro="color_coverage_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1121
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1122 <expand macro="minmax_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1123
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1124 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1125 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1126 <param name="summary_method" type="select" label="Summary method">
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1127 <option value="mean" selected="True">mean=mean value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1128 <option value="min">min=minimum value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1129 <option value="max">max=maximum value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1130 <option value="coverage">coverage=number of covered bases</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1131 <option value="std">std=standard deviation</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1132 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1133 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1134 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1135 label="NAN's to zeros" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1136 </section>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1137 <expand macro="type_coverage_macro" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1138 <expand macro="logScale_coverage_macro" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1139 <section name ="op" title="Compute an operation on the file" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1140 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1141 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1142 <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1143 </section>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1144 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1145 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1146 <expand macro="inverted_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1147 <expand macro="overlay_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1148 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1149
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1150 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1151
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1152 <when value="bedgraph_matrix_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1153 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1154
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1155 <expand macro="track_input_bedgraph_matrix_macro" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1156 <expand macro="minmax_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1157
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1158 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1159
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1160 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1161 <param name="type_selector" type="select" label="type of plotting">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1162 <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1163 <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1164 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1165 <when value="lines">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1166 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1167 label="Plot an horizontal line at 0 when type is lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1168 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1169 label="Show visualization of data range" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1170 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1171 <option value="center" selected="True">Center</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1172 <option value="block">Block (draw a horizontal line between start and end)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1173 </param>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1174 <param name="individual_color" type="color" value="grey" label="Color of the individual lines" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1175 <param name="summary_color" type="color" value="#1f77b4" label="Color of the summary line" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1176 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1177 <when value="matrix">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1178 <param name="colormap" type="select" label="colormap">
10
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1179 <option value="viridis">viridis</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1180 <option value="RdYlBu_r">RdYlBu reversed</option>
a1abfa420d9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"
iuc
parents: 9
diff changeset
1181 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1182 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1183 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1184 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1185
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1186
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1187 <expand macro="inverted_macro" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1188 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1189
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1190 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1191 <when value="vlines_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1192 <expand macro="track_input_bed_single_macro" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1193 <param name="line_width" type="float" value="0.5" label="width of lines"/>
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1194 <param name="line_style" type="select" label="Line Style">
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1195 <option value="dashed">Dashed</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1196 <option value="solid">Solid</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1197 <option value="dotted">Dotted</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1198 <option value="dashdot">Dashdot</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1199 </param>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1200 <param name="color" type="color" value="black" label="color of the vline"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1201 <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1202 <param name="zorder" type="select" label="Plot the vline above or behind other tracks">
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1203 <option value="100">above</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1204 <option value="-100">behind</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1205 </param>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1206 </when>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1207 <when value="vhighlight_track_option">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1208 <expand macro="track_input_bed_single_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1209 <param name="color" type="color" value="yellow" label="color of the highlight"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1210 <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/>
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1211 <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" />
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1212 <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1213 <param name="zorder" type="select" label="Plot the highlight above or behind other tracks">
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1214 <option value="-100">behind</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1215 <option value="100">above</option>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
1216 </param>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1217 </when>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1218 <when value="hlines_track_option">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1219 <expand macro="plot_title" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1220 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1221 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1222 <expand macro="lines_macro" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1223 <param name="height" type="float" value="1.5" optional="True" label="height of the Hlines track"/>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1224 <expand macro="minmax_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1225 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1226 <expand macro="inverted_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1227 <expand macro="overlay_macro" />
6
5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents: 5
diff changeset
1228 <expand macro="spacer_macro" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1229 </when>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1230 <when value="spacer_option">
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1231 <expand macro="plot_title" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1232 <param name="spacer_height" type="float" value="" optional="True"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1233 label="Height of the spacer."/>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1234 </when>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1235 <when value="xaxis_option">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1236 <expand macro="plot_title" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1237 <param name="fontsize" type="float" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1238 label="Fontsize of the x-axis."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1239 <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1240 <option value="bottom" selected="True">below</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1241 <option value="top">above</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1242 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1243 <expand macro="spacer_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1244 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1245 <when value="scale_bar_option">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1246 <expand macro="plot_title" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1247 <param name="color" type="color" label="Color of the scale bar" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1248 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1249 <param name="line_width" type="float" value="0.5" label="width of lines"/>
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1250 <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below.">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1251 <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1252 <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1253 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1254 help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1255 <param name="size" type="integer" label="size of the scale bar" optional="True"
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1256 help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1257 </section>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1258 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1259 <option value="left" selected="True">left</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1260 <option value="right">right</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1261 <option value="bottom">below</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1262 <option value="top">above</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1263 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1264 <param name="fontsize" type="float" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1265 label="Fontsize of the size of the scale bar."/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1266 <param name="height" type="float" value="0.5" optional="True" label="height of the Scale bar track"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1267 <expand macro="spacer_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1268 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1269 <when value="fasta_option">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1270 <expand macro="track_input_fasta_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1271 <expand macro="plot_title" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1272 <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1273 <expand macro="inverted_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1274 <expand macro="overlay_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1275 <expand macro="spacer_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1276 </when>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1277 <when value="maf_option">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1278 <expand macro="track_input_maf_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1279 <expand macro="plot_title" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1280 <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1281 <param name="reference" type="select" label="Reference">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1282 <options>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1283 <filter type="data_meta" ref="track_input_maf" key="species" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1284 </options>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1285 </param>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1286 <param name="line_width" type="float" value="0.5" label="width of lines"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1287 <param name="color_identical" type="color" label="Color when bases are identical" value="black" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1288 <param name="color_mismatch" type="color" label="Color when bases are different" value="grey" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1289 <param name="color_gap" type="color" label="Color when bases corresponds to gap" value="lightgrey" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1290 <param name="species_order" type="text" value="" label="[Optional] The order you want your species (space separated)"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1291 help="checkout the choices for reference to see available species"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1292 <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1293 <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1294 label="Display only the species specified above"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1295 <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false"
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1296 label="Display the sequence of the reference"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1297 <expand macro="inverted_macro" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1298 <expand macro="overlay_macro" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1299 <expand macro="spacer_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1300 </when>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1301 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1302 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1303 <param name="image_file_format" type="select" label="Image output format">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1304 <option value="png">png</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1305 <option value="svg">svg</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1306 </param>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1307 </inputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1308 <outputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1309 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1310 <change_format>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1311 <when input="image_file_format" value="png" format="png" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1312 <when input="image_file_format" value="svg" format="svg" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1313 </change_format>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1314 </data>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1315 </outputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1316 <tests>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1317 <!--test 1-->
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1318 <test>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1319 <param name="region" value="chrX:3000000-3500000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1320 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1321 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1322 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1323 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1324 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1325 </repeat>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1326 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1327 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1328 <param name="track_file_style_selector" value="hic_matrix_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1329 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1330 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1331 <!--<param name="colormap" value="RdYlBu_r" />-->
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1332 <param name="depth" value="200000" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1333 <param name="transform" value="log1p" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1334 <param name="boundaries_file" value="domains.bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1335 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1336 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1337 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1338 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1339 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1340 <param name="spacer_height" value="0.05" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1341 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1342 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1343 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1344 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1345 <param name="track_file_style_selector" value="chrom_states_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1346 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1347 <param name="title" value="TAD state" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1348 <param name="height_chrom" value="0.5" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1349 <param name="labels" value="false" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1350 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1351 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1352 </conditional>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1353 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1354 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1355 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1356 <conditional name="track_file_style_conditional">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1357 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1358 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1359 <param name="title" value="TAD separation score (Ramirez et al.)" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1360 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1361 <param name="type_selector" value="matrix" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1362 <!--<param name="colormap" value="viridis" />-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1363 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1364 <param name="height_bedgraph" value="10" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1365 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1366 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1367 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1368 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1369 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1370 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1371 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1372 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1373 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1374 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1375 <param name="track_file_style_selector" value="bedgraph_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1376 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1377 <param name="title" value="bedgraph" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1378 <param name="height_bedgraph" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1379 <param name="color" value="blue" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1380 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1381 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1382 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1383 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1384 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1385 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1386 <param name="title" value="rep 1 test fill" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1387 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1388 <param name="color" value="blue" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1389 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1390 <param name="type_selector" value="fill_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1391 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1392 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1393 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1394 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1395 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1396 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1397 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1398 <param name="title" value="rep 1 test line" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1399 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1400 <param name="color" value="red" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1401 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1402 <param name="type_selector" value="line_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1403 <param name="width_line" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1404 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1405 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1406 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1407 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1408 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1409 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1410 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1411 <param name="title" value="rep 1 test lw=0.2" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1412 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1413 <param name="color" value="red" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1414 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1415 <param name="type_selector" value="line_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1416 <param name="width_line" value="0.1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1417
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1418 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1419 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1420 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1421 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1422 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1423 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1424 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1425 <param name="title" value="rep 1 test point:0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1426 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1427 <param name="color" value="black" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1428 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1429 <param name="type_selector" value="point_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1430 <param name="width_point" value="0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1431
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1432 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1433 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1434 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1435 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1436 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1437 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1438 <param name="spacer_height" value="0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1439 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1440 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1441 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1442 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1443 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1444 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1445 <param name="title" value="genes" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1446 <param name="height_bed" value="5" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1447 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1448 <param name="fontsize" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1449 </conditional>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1450 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1451 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1452 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1453 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1454 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1455 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1456 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1457 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1458 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1459 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1460 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1461 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1462 <param name="title" value="max num rows 3" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1463 <param name="height_bed" value="3" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1464 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1465 <param name="fontsize" value="8" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1466 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1467 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1468 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1469 <param name="gene_rows" value="3" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1470 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1471 </conditional>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1472 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1473 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1474 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1475 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1476 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1477 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1478 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1479 </repeat>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1480 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1481 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1482 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1483 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1484 <param name="title" value="bed6 global max row" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1485 <param name="height_bed" value="20" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1486 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1487 <param name="fontsize" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1488 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1489 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1490 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1491 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1492 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1493 </conditional>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1494 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1495 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1496 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1497 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1498 <param name="track_file_style_selector" value="vlines_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1499 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1500 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1501 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1502 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1503 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="100" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1504 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1505 <!--test 2-->
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1506 <test>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1507 <param name="region" value="chrX:3000000-3500000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1508 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1509 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1510 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1511 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1512 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1513 </repeat>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1514 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1515 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1516 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1517 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1518 <param name="title" value="rep 1 test line" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1519 <param name="height_bigwig" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1520 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1521 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1522 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1523 <param name="width_line" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1524 </conditional>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1525 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1526 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1527 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1528 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1529 <param name="track_file_style_selector" value="bigwig_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1530 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1531 <param name="title" value="nans_to_zeros" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1532 <param name="height_bigwig" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1533 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1534 <section name="reading_bw_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1535 <param name="nans_to_zeros" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1536 </section>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1537 <param name="show_data" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1538 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1539 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1540 <param name="width_line" value="1" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1541 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1542 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1543 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1544 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1545 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1546 <param name="track_file_style_selector" value="hlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1547 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1548 <param name="color" value="orange" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1549 <param name="y_values" value="50" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1550 <param name="line_width" value="2" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1551 <param name="line_style" value="dashed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1552 <param name="overlay_select" value="share-y" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1553 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1554 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1555 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1556 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1557 <param name="track_file_style_selector" value="hlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1558 <param name="title" value="hlines" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1559 <param name="color" value="purple" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1560 <param name="y_values" value="0, 10, 20, 100" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1561 <param name="min_value" value="12" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1562 <param name="show_data" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1563 <param name="invert_orientation" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1564 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1565 </repeat>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1566 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1567 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="100" />
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
1568 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1569 <!--test 3-->
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1570 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1571 <param name="region" value="chrX:3000000-3500000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1572 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1573 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1574 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1575 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1576 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1577 </repeat>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1578 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1579 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1580 <param name="track_file_style_selector" value="hic_matrix_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1581 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1582 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1583 <param name="colormap" value="RdYlBu_r" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1584 <param name="depth" value="200000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1585 <param name="transform" value="log1p" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1586 <param name="boundaries_file" value="domains.bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1587 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1588 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1589 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1590 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1591 <param name="track_file_style_selector" value="chrom_states_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1592 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1593 <param name="title" value="TAD state" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1594 <param name="height_chrom" value="0.5" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1595 <param name="labels" value="false" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1596 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1597 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1598 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1599 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1600 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1601 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1602 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1603 <param name="track_file_style_selector" value="hic_matrix_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1604 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1605 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1606 <param name="colormap" value="Reds" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1607 <param name="depth" value="200000" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1608 <param name="transform" value="no" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1609 <param name="invert_orientation" value="true" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1610 <param name="min_value" value="5" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1611 <param name="max_value" value="70" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1612 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1613 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1614 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1615 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1616 <param name="track_file_style_selector" value="spacer_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1617 <param name="spacer_height" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1618 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1619 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1620 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1621 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1622 <param name="track_file_style_selector" value="bedgraph_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1623 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1624 <param name="title" value="bedgraph with negative values" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1625 <param name="height_bedgraph" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1626 <param name="color" value="black" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1627 <conditional name="color_negative">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1628 <param name="color_negative_select" value="true" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1629 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1630 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1631 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1632 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1633 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1634 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1635 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1636 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1637 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1638 <param name="track_file_style_selector" value="bedgraph_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1639 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1640 <param name="title" value="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1641 <param name="height_bedgraph" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1642 <param name="color" value="blue" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1643 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1644 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1645 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1646 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1647 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1648 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1649 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1650 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1651 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1652 <param name="title" value="rep 1 test fill" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1653 <param name="height_bigwig" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1654 <param name="color" value="blue" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1655 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1656 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1657 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1658 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1659 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1660 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1661 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1662 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1663 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1664 <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1665 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1666 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1667 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1668 <param name="type_selector" value="point_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1669 <param name="width_point" value="5" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1670 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1671 <section name="reading_bw_conditional">
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1672 <param name="summary_method" value="max"/>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1673 <param name="number_of_bins" value="100"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1674 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1675 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1676 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1677 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1678 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1679 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1680 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1681 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1682 <param name="color" value="#c00000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1683 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1684 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1685 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1686 <section name="reading_bw_conditional">
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1687 <param name="summary_method" value="min"/>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1688 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1689 <param name="overlay_select" value="share-y" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1690 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1691 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1692 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1693 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1694 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1695 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1696 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1697 <param name="color" value="black" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1698 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1699 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1700 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1701 <section name="reading_bw_conditional">
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1702 <param name="summary_method" value="min"/>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1703 <param name="number_of_bins" value="30000"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1704 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1705 <param name="overlay_select" value="share-y" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1706 <param name="spacer_height" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1707 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1708 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1709 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1710 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1711 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1712 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1713 <param name="title" value="genes in ucsc" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1714 <param name="height_bed" value="5" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1715 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1716 <param name="fontsize" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1717 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1718 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1719 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1720 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1721 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1722 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1723 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1724 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1725 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1726 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1727 <param name="title" value="bed6 global max row color from score" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1728 <param name="height_bed" value="20" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1729 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1730 <param name="fontsize" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1731 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1732 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1733 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1734 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1735 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1736 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1737 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1738 <param name="color_bed_select" value="colormap" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1739 <param name="color" value="RdYlBu_r" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1740 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1741 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1742 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1743 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1744 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1745 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1746 <param name="track_input_bed" value="domains.bed" ftype="bed" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1747 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1748 <param name="height_bed" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1749 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1750 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1751 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1752 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1753 <param name="border_color_bed_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1754 <param name="color" value="red" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1755 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1756 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1757 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1758 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1759 <param name="display" value="interleaved" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1760 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1761 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1762 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1763 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1764 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1765 <param name="track_input_bed" value="domains.bed" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1766 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1767 <param name="height_bed" value="2" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1768 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1769 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1770 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1771 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1772 <param name="border_color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1773 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1774 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1775 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1776 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1777 <param name="display" value="interleaved" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1778 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1779 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1780 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1781 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1782 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1783 <param name="track_input_bed" value="domains.bed" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1784 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1785 <param name="height_bed" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1786 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1787 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1788 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1789 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1790 <param name="border_color_bed_select" value="none" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1791 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1792 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1793 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1794 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1795 <param name="display" value="interleaved" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1796 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1797 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1798 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1799 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="100" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1800 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1801 <!--test 4-->
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1802 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1803 <param name="region" value="X:2700000-3100000"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1804 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1805 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1806 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1807 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1808 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1809 <param name="height_bigwig" value="7" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1810 <param name="color" value="#00b0f0" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1811 <section name="reading_bw_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1812 <param name="number_of_bins" value="2000"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1813 </section>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1814 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1815 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1816 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1817 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1818 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1819 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1820 <param name="title" value="" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1821 <param name="color" value="#ff0000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1822 <param name="alpha" value="0.5" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
1823 <param name="summary_method" value="max" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1824 <section name="reading_bw_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1825 <param name="number_of_bins" value="300"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1826 </section>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1827 <param name="overlay_select" value="share-y"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1828 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1829 </repeat>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1830 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1831 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1832 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1833 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1834 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1835 </repeat>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1836 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1837 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="100" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1838 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1839 <!--test 5-->
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1840 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1841 <param name="region" value="X:3000000-3300000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1842 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1843 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1844 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1845 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1846 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1847 </repeat>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1848 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1849 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1850 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1851 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1852 <param name="title" value="test" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1853 <param name="height_bed" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1854 <param name="color" value="#000000" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1855 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1856 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1857 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1858 <param name="spacer_height" value="1"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1859 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1860 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1861 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1862 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1863 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1864 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1865 <param name="title" value="test" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1866 <param name="height_bed" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1867 <param name="color" value="#000000" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1868 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1869 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1870 </conditional>
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1871 <param name="spacer_height" value="1"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1872 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1873 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1874 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1875 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="100" />
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
1876 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1877 <!--test 6-->
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1878 <test>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1879 <param name="region" value="X:2760000-2802000"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1880 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1881 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1882 <param name="track_file_style_selector" value="narrow_peak_track_option" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1883 <param name="title" value="box" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1884 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1885 <param name="color" value="#9bbb59" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1886 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1887 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1888 <param name="display_selector" value="box" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1889 <param name="use_summit" value="true" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1890 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1891 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1892 </repeat>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1893 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1894 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1895 <param name="track_file_style_selector" value="narrow_peak_track_option" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1896 <param name="title" value="box line_width = 2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1897 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1898 <param name="color" value="#9bbb59" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1899 <param name="height_narrow_peak" value="4" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1900 <param name="line_width" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1901 <conditional name="display">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1902 <param name="display_selector" value="box" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1903 <param name="use_summit" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1904 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1905 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1906 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1907 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1908 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1909 <param name="track_file_style_selector" value="narrow_peak_track_option" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1910 <param name="title" value="peak width 3" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1911 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1912 <param name="color" value="#c0504d" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1913 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1914 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1915 <param name="display_selector" value="peak" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1916 <param name="use_summit" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1917 <param name="show_data" value="true" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1918 <param name="width_adjust" value="3" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1919 <param name="max_value" value="50" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1920 </conditional>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1921 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1922 <param name="show_labels" value="false" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1923 </conditional>
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1924 <param name="spacer_height" value="0.5"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1925 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1926 </repeat>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1927 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1928 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1929 <param name="track_file_style_selector" value="narrow_peak_track_option" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1930 <param name="title" value="peak no data range" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1931 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1932 <param name="color" value="#000000" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1933 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1934 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1935 <param name="display_selector" value="peak" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1936 <param name="use_summit" value="false" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1937 <param name="show_data" value="false" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1938 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1939 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1940 </repeat>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1941 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1942 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1943 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1944 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1945 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1946 </repeat>
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1947 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
1948 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="100" />
4
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents: 3
diff changeset
1949 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1950 <!--test 7-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1951 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1952 <param name="region" value="chrX:3300000-3500000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1953 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1954 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1955 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1956 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1957 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1958 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1959 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1960 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1961 <param name="track_file_style_selector" value="gene_track_option" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1962 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1963 <param name="title" value="gtf default" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1964 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1965 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1966 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1967 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1968 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1969 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1970 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1971 <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1972 <param name="height_bed" value="10" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1973 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1974 <section name="bed_advanced">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
1975 <param name="height_utr" value="0.75"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1976 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1977 <param name="color_utr_select" value="manually"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1978 <param name="color" value="#ff0000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1979 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1980 <section name ="gtf">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
1981 <param name="prefered_name" value="gene_name"/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1982 <conditional name="merge_transcripts">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1983 <param name="merge_transcripts_select" value="true"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1984 <param name="merge_overlapping_exons" value="false"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1985 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1986 </section>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1987 </section>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1988 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1989 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1990 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1991 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1992 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1993 <param name="track_file_style_selector" value="gene_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1994 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1995 <param name="title" value="same but merge overlapping exons" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1996 <param name="height_bed" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1997 <conditional name="bed_style">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1998 <section name="bed_advanced">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
1999 <param name="height_utr" value="0.75"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2000 <conditional name="color_utr">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2001 <param name="color_utr_select" value="manually"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2002 <param name="color" value="#ff0000"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2003 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2004 <section name ="gtf">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2005 <param name="prefered_name" value="gene_name"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2006 <conditional name="merge_transcripts">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2007 <param name="merge_transcripts_select" value="true"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2008 <param name="merge_overlapping_exons" value="true"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2009 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2010 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2011 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2012 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2013 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2014 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2015 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2016 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2017 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2018 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2019 <param name="title" value="genes with scores" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2020 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2021 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2022 <param name="color_bed_select" value="colormap" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2023 <param name="color" value="cool_r" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2024 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2025 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2026 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2027 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2028 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2029 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2030 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2031 <param name="title" value="genes with utr as bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2032 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2033 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2034 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2035 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2036 <param name="color_utr_select" value="bed_rgb"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2037 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2038 </section>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2039 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2040 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2041 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2042 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2043 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2044 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2045 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2046 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2047 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2048 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2049 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2050 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2051 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2052 <param name="plot_labels" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2053 <param name="labels_in_margin" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2054 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2055 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2056 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2057 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2058 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2059 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2060 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2061 <param name="title" value="genes bed_rgb like - all_labels_inside" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2062 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2063 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2064 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2065 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2066 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2067 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2068 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2069 <param name="color_utr_select" value="like"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2070 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2071 </section>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2072 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2073 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2074 <param name="plot_labels" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2075 <param name="all_labels_inside" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2076 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2077 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2078 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2079 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2080 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2081 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2082 <!--test 8-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2083 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2084 <param name="region" value="chrX:3300000-3500000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2085 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2086 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2087 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2088 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2089 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2090 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2091 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2092 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2093 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2094 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2095 <param name="title" value="dm3_genes.bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2096 <param name="height_bed" value="10" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2097 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2098 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2099 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2100 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2101 <param name="max_labels" value="15" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2102 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2103 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2104 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2105 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2106 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2107 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2108 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2109 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2110 <param name="title" value="genes.bed.gz" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2111 <param name="height_bed" value="10" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2112 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2113 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2114 <section name="bed_advanced">
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2115 <param name="arrow_interval" value="10"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2116 <param name="line_width" value="2"/>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2117 </section>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2118 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2119 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2120 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2121 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2122 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2123 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2124 <!--test 9-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2125 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2126 <param name="region" value="X:3133000-3138000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2127 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2128 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2129 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2130 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2131 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2132 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2133 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2134 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2135 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2136 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2137 <param name="title" value="defaut arrowhead fontstyle italic" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2138 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2139 <param name="spacer_height" value="1"/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2140 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2141 <param name="fontstyle" value="italic"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2142 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2143 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2144 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2145 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2146 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2147 <param name="track_file_style_selector" value="gene_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2148 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2149 <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2150 <param name="height_bed" value="10" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2151 <param name="spacer_height" value="1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2152 <conditional name="labels">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2153 <param name="fontstyle" value="oblique"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2154 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2155 <conditional name="bed_style">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2156 <param name="arrowhead_fraction" value="0.1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2157 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2158 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2159 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2160 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2161 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2162 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2163 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2164 <param name="title" value="genes without orientation" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2165 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2166 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2167 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2168 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2169 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2170 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2171 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2172 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2173 <param name="spacer_height" value="1"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2174 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2175 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2176 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2177 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2178 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2179 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2180 <param name="title" value="arrowhead included" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2181 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2182 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2183 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2184 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2185 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2186 <param name="spacer_height" value="1"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2187 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2188 <param name="arrowhead_included" value="true"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2189 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2190 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2191 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2192 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2193 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2194 <param name="track_file_style_selector" value="vlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2195 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2196 <param name="line_width" value="2"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2197 <param name="zorder" value="100"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2198 <param name="color" value="red"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2199 </conditional>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2200 </repeat>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2201 <repeat name="tracks">
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2202 <conditional name="track_file_style_conditional">
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2203 <param name="track_file_style_selector" value="vlines_track_option" />
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2204 <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" />
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2205 <param name="line_width" value="5"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2206 <param name="zorder" value="-100"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2207 <param name="color" value="blue"/>
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
iuc
parents: 11
diff changeset
2208 <param name="line_style" value="solid"/>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2209 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2210 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2211 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2212 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2213 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2214 <!--test 10-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2215 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2216 <param name="region" value="X:3340000-3380000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2217 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2218 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2219 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2220 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2221 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2222 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2223 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2224 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2225 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2226 <param name="track_input_bed" value="domains.bed" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2227 <param name="height_bed" value="6" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2228 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2229 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2230 <param name="color" value="yellow" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2231 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2232 <param name="display" value="triangles" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2233 <param name="spacer_height" value="1"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2234 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2235 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2236 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2237 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2238 <param name="track_file_style_selector" value="bedgraph_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2239 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2240 <param name="title" value="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2241 <param name="height_bedgraph" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2242 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2243 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2244 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2245 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2246 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2247 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2248 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2249 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2250 <param name="track_file_style_selector" value="bedgraph_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2251 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2252 <param name="title" value="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2253 <param name="height_bedgraph" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2254 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2255 <param name="use_middle" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2256 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2257 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2258 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2259 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2260 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2261 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2262 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2263 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2264 <!--test 11-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2265 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2266 <param name="region" value="chrX:3250000-3400000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2267 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2268 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2269 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2270 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2271 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2272 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2273 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2274 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2275 <param name="track_file_style_selector" value="hic_matrix_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2276 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2277 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2278 <!--<param name="colormap" value="RdYlBu_r" />-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2279 <param name="depth" value="100000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2280 <param name="transform" value="log1p" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2281 <param name="show_masked_bins" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2282 <param name="scale_factor" value="2.0" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2283 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2284 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2285 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2286 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2287 <param name="track_file_style_selector" value="spacer_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2288 <param name="spacer_height" value="0.05" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2289 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2290 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2291 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2292 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2293 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2294 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2295 <param name="title" value="TAD separation score (Ramirez et al.) as block with horizontal lines and data range" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2296 <param name="height_bedgraph" value="10" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2297 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2298 <param name="type_selector" value="lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2299 <param name="pos_score_in_bin" value="block" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2300 <param name="plot_horizontal_lines" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2301 <param name="show_data" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2302 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2303 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2304 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2305 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2306 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2307 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2308 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2309 <param name="title" value="TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2310 <param name="height_bedgraph" value="10" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2311 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2312 <param name="type_selector" value="lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2313 <param name="pos_score_in_bin" value="center" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2314 <param name="plot_horizontal_lines" value="false" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2315 <param name="individual_color" value="blue"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2316 <param name="summary_color" value="red"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2317 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2318 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2319 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2320 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2321 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2322 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2323 <!--test 12-->
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2324 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2325 <param name="region" value="chrX:3000000-3300000"/>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2326 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2327 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2328 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2329 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2330 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2331 </repeat>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2332 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2333 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2334 <param name="track_file_style_selector" value="hic_matrix_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2335 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2336 <param name="title" value="Kc DpnII (Li et al. 2015)" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2337 <param name="colormap" value="Purples" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2338 <param name="depth" value="190000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2339 <param name="transform" value="no" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2340 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2341 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2342 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2343 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2344 <param name="track_file_style_selector" value="link_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2345 <param name="track_input_link" value="test.arcs" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2346 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2347 <param name="line_width" value="10" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2348 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2349 <param name="links_type" value="loops" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2350 </conditional>
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2351 <conditional name="color_link">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2352 <param name="color_link_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2353 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2354 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2355 <param name="overlay_select" value="share-y" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2356 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2357 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2358 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2359 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2360 <param name="track_file_style_selector" value="link_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2361 <param name="track_input_link" value="test.arcs" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2362 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2363 <param name="height" value="5" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2364 <conditional name="color_link">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2365 <param name="color_link_select" value="colormap" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2366 <param name="color" value="hot" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2367 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2368 <param name="max_value" value="5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2369 <param name="invert_orientation" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2370 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2371 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2372 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2373 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="100" />
5
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents: 4
diff changeset
2374 </test>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2375 <!--test 13-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2376 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2377 <param name="region" value="chrX:3000000-3300000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2378 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2379 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2380 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2381 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2382 <param name="title" value="default" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2383 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2384 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2385 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2386 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2387 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2388 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2389 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2390 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2391 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2392 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2393 <param name="title" value="ylim 20kb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2394 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2395 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2396 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2397 </conditional>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2398 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2399 <param name="ylim" value="20000" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2400 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2401 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2402 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2403 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2404 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2405 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2406 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2407 <param name="title" value="compacted" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2408 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2409 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2410 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2411 </conditional>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2412 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2413 <param name="compact_arcs_level" value="1" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2414 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2415 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2416 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2417 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2418 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2419 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2420 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2421 <param name="title" value="highly compacted" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2422 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2423 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2424 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2425 </conditional>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2426 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2427 <param name="compact_arcs_level" value="2" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2428 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2429 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2430 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2431 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2432 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="100" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2433 </test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2434 <!--test 14-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2435 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2436 <param name="region" value="chrX:3000000-3300000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2437 <section name="global_args">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2438 <param name="title" value="Scale bar"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2439 <param name="trackLabelFraction" value="0.5"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2440 <param name="trackLabelHAlign" value="center"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2441 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2442 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2443 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2444 <param name="track_file_style_selector" value="spacer_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2445 <param name="spacer_height" value="1.0" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2446 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2447 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2448 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2449 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2450 <param name="track_file_style_selector" value="scale_bar_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2451 <param name="title" value="default" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2452 <param name="spacer_height" value="1"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2453 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2454 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2455 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2456 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2457 <param name="track_file_style_selector" value="scale_bar_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2458 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2459 <param name="color" value="red"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2460 <param name="alpha" value="0.5"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2461 <param name="line_width" value="2"/>
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2462 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2463 <param name="x_center" value="3200000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2464 <param name="size" value="100002"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2465 </section>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2466 <param name="sb_where" value="right"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2467 <param name="fontsize" value="8"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2468 <param name="spacer_height" value="4"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2469 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2470 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2471 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2472 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="100" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2473 </test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2474 <!--test 15-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2475 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2476 <param name="region" value="chrX:3300000-3500000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2477 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2478 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2479 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2480 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2481 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2482 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2483 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2484 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2485 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2486 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2487 <param name="title" value="flybase backbone blue" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2488 <param name="height_bed" value="10" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2489 <conditional name="bed_style">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2490 <param name="bed_style_select" value="flybase"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2491 <section name="bed_advanced">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2492 <conditional name="backbone_color_bed">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2493 <param name="backbone_color_bed_select" value="manually" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2494 <param name="color" value="blue" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2495 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2496 </section>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2497 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2498 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2499 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2500 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2501 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2502 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2503 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2504 <param name="title" value="UCSC backbone blue" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2505 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2506 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2507 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2508 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2509 <param name="arrow_interval" value="10"/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2510 <conditional name="backbone_color_bed">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2511 <param name="backbone_color_bed_select" value="manually" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2512 <param name="color" value="blue" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2513 </conditional>
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2514 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2515 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2516 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2517 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2518 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2519 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2520 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2521 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2522 <param name="title" value="tssarrow" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2523 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2524 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2525 <param name="bed_style_select" value="tssarrow"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2526 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2527 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2528 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2529 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2530 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2531 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2532 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2533 <param name="title" value="tssarrow 5kb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2534 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2535 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2536 <param name="bed_style_select" value="tssarrow"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2537 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2538 <param name="arrow_length" value="5000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2539 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2540 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2541 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2542 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2543 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2544 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="100" />
7
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents: 6
diff changeset
2545 </test>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2546 <!--test 16-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2547 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2548 <param name="region" value="X:2700000-3100000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2549 <section name="global_args">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2550 <param name="decreasingXAxis" value="true"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2551 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2552 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2553 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2554 <param name="track_file_style_selector" value="bigwig_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2555 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2556 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2557 <param name="height_bigwig" value="7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2558 <param name="color" value="#00b0f0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2559 <section name="reading_bw_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2560 <param name="number_of_bins" value="2000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2561 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2562 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2563 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2564 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2565 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2566 <param name="track_file_style_selector" value="bigwig_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2567 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2568 <param name="title" value="" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2569 <param name="color" value="#ff0000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2570 <param name="alpha" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2571 <param name="summary_method" value="max" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2572 <section name="reading_bw_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2573 <param name="number_of_bins" value="300"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2574 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2575 <param name="overlay_select" value="share-y"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2576 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2577 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2578 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2579 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2580 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2581 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2582 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2583 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2584 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2585 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="1000" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2586 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2587 <!--test 17-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2588 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2589 <param name="region" value="chr2:73,800,000-75,744,000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2590 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2591 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2592 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2593 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2594 <param name="title" value="bedgraph color = blue transform = no" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2595 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2596 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2597 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2598 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2599 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2600 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2601 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2602 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2603 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2604 <param name="title" value="bedgraph color = blue transform = log" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2605 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2606 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2607 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2608 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2609 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2610 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2611 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2612 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2613 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2614 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2615 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2616 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2617 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2618 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2619 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2620 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2621 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2622 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2623 <param name="min_value" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2624 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2625 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2626 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2627 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2628 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2629 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2630 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2631 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2632 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2633 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2634 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2635 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2636 <param name="log_pseudocount" value="2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2637 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2638 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2639 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2640 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2641 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2642 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2643 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2644 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2645 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2646 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2647 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2648 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2649 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2650 <param name="operation" value="log(2+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2651 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2652 <param name="min_value" value="0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2653 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2654 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2655 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2656 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2657 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2658 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2659 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2660 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2661 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2662 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2663 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2664 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2665 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2666 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2667 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2668 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2669 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2670 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2671 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2672 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2673 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2674 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2675 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2676 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2677 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2678 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2679 <param name="operation" value="log2(1+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2680 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2681 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2682 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2683 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2684 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2685 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2686 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2687 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2688 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2689 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2690 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2691 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2692 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2693 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2694 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2695 <param name="y_axis_values" value="original"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2696 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2697 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2698 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2699 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2700 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2701 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2702 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2703 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2704 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2705 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2706 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2707 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2708 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="100" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2709 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2710 <!--test 18-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2711 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2712 <param name="region" value="chrX:2700000-3100000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2713 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2714 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2715 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2716 <param name="xaxis_where" value="top" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2717 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2718 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2719 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2720 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2721 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2722 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2723 <param name="title" value="file summary_method = mean number_of_bins=20" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2724 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2725 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2726 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2727 <section name="reading_bdg_as_bw" >
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2728 <param name="summary_method" value="mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2729 <param name="number_of_bins" value="20" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2730 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2731 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2732 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2733 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2734 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2735 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2736 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2737 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2738 <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2739 <param name="title" value="second_file summary_method = mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2740 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2741 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2742 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2743 <section name="reading_bdg_as_bw" >
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2744 <param name="summary_method" value="mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2745 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2746 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2747 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2748 <param name="spacer_height" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2749 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2750 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2751 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2752 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2753 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2754 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2755 <param name="title" value="operation = log1p(file) (no summary_method)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2756 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2757 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2758 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2759 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2760 <param name="operation" value="log1p(file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2761 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2762 <param name="spacer_height" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2763 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2764 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2765 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2766 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2767 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2768 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2769 <param name="title" value="operation = file - second_file" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2770 <param name="height_bedgraph" value="8" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2771 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2772 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2773 <conditional name="color_negative">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2774 <param name="color_negative_select" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2775 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2776 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2777 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2778 <param name="operation" value="file - second_file" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2779 <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2780 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2781 <param name="min_value" value="-30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2782 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2783 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2784 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2785 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2786 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="100" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2787 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2788 <!--test 19-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2789 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2790 <param name="region" value="chr2:73,800,000-75,744,000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2791 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2792 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2793 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2794 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2795 <param name="title" value="bedgraph color = blue transform = no" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2796 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2797 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2798 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2799 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2800 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2801 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2802 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2803 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2804 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2805 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2806 <param name="title" value="bedgraph color = blue transform = log" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2807 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2808 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2809 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2810 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2811 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2812 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2813 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2814 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2815 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2816 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2817 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2818 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2819 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2820 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2821 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2822 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2823 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2824 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2825 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2826 <param name="min_value" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2827 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2828 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2829 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2830 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2831 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2832 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2833 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2834 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2835 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2836 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2837 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2838 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2839 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2840 <param name="log_pseudocount" value="2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2841 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2842 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2843 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2844 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2845 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2846 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2847 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2848 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2849 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2850 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2851 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2852 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2853 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2854 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2855 <param name="operation" value="log(2+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2856 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2857 <param name="min_value" value="0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2858 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2859 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2860 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2861 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2862 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2863 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2864 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2865 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2866 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2867 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2868 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2869 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2870 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2871 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2872 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2873 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2874 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2875 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2876 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2877 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2878 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2879 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2880 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2881 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2882 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2883 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2884 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2885 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2886 <param name="operation" value="log2(1+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2887 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2888 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2889 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2890 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2891 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2892 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2893 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2894 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2895 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2896 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2897 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2898 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2899 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2900 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2901 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2902 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2903 <param name="y_axis_values" value="original"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2904 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2905 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2906 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2907 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2908 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2909 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2910 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2911 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2912 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2913 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2914 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2915 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2916 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2917 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="100" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2918 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2919 <!--test 20-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2920 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2921 <param name="region" value="chrX:3000000-3300000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2922 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2923 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2924 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2925 <param name="xaxis_where" value="top" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2926 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2927 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2928 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2929 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2930 <param name="track_file_style_selector" value="spacer_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2931 <param name="spacer_height" value="0.05" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2932 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2933 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2934 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2935 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2936 <param name="track_file_style_selector" value="hic_matrix_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2937 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2938 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2939 <param name="depth" value="300000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2940 <param name="transform" value="log1p" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2941 <param name="min_value" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2942 <param name="show_masked_bins" value="false" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2943 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2944 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2945 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2946 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2947 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2948 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2949 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2950 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2951 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2952 <param name="line_width" value="5" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2953 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2954 <param name="links_type" value="loops" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2955 </conditional>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2956 <param name="overlay_select" value="share-y" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2957 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2958 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2959 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2960 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2961 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2962 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2963 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2964 <param name="color" value="RdYlGn" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2965 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2966 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2967 <param name="invert_orientation" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2968 <param name="title" value="links line_width = 3 color RdYlGn" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
2969 <param name="height" value="3" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2970 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2971 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2972 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2973 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2974 <param name="track_file_style_selector" value="spacer_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2975 <param name="spacer_height" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2976 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2977 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2978 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2979 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2980 <param name="track_file_style_selector" value="hic_matrix_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2981 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2982 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2983 <param name="depth" value="300000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2984 <param name="transform" value="log1p" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2985 <param name="min_value" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2986 <param name="show_masked_bins" value="false" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2987 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2988 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2989 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2990 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2991 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2992 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2993 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2994 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2995 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
2996 <param name="line_width" value="5" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2997 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2998 <param name="links_type" value="loops" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
2999 </conditional>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3000 <param name="overlay_select" value="share-y" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3001 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3002 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3003 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3004 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3005 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3006 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3007 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3008 <param name="color" value="RdYlGn" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3009 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3010 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3011 <param name="invert_orientation" value="true" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3012 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3013 <param name="use_middle" value="true" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3014 </conditional>
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3015 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3016 <param name="height" value="3" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3017 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3018 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3019 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3020 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3021 <param name="track_file_style_selector" value="vlines_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3022 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3023 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3024 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3025 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3026 <param name="image_file_format" value="png" />
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3027 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="1200" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3028 </test>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3029 <!--test 21-->
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3030 <test>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3031 <param name="region" value="X:3000000-3600000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3032 <section name="global_args">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3033 <param name="trackLabelFraction" value="0.3"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3034 <param name="plotWidth" value="12"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3035 <param name="dpi" value="20"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3036 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3037 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3038 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3039 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3040 <param name="title" value="scalebar where = right" />
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3041 <param name="sb_where" value="right"/>
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3042 <param name="spacer_height" value="0.5"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3043 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3044 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3045 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3046 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3047 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3048 <param name="title" value="scalebar scalebar_start_position = 3200000" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3049 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3050 <param name="scalebar_start_position" value="3200000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3051 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3052 <param name="spacer_height" value="0.5"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3053 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3054 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3055 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3056 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3057 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3058 <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3059 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3060 <param name="scalebar_start_position" value="3200000"/>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3061 <param name="scalebar_end_position" value="3250000"/>
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3062 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3063 <param name="spacer_height" value="0.5"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3064 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3065 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3066 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3067 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3068 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3069 <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3070 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3071 <param name="scalebar_start_position" value="3200000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3072 <param name="x_center" value="3250000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3073 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3074 <param name="spacer_height" value="0.5"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3075 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3076 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3077 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3078 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3079 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3080 <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3081 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3082 <param name="scalebar_start_position" value="3200000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3083 <param name="size" value="50000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3084 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3085 <param name="spacer_height" value="0.5"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3086 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3087 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3088 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3089 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3090 <param name="track_file_style_selector" value="scale_bar_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3091 <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3092 <section name="scalebar_pos">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3093 <param name="scalebar_end_position" value="3200000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3094 <param name="size" value="50000"/>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3095 </section>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3096 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3097 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3098 <repeat name="tracks">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3099 <conditional name="track_file_style_conditional">
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3100 <param name="track_file_style_selector" value="xaxis_option" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3101 <param name="xaxis_where" value="bottom" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3102 </conditional>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3103 </repeat>
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3104 <param name="image_file_format" value="png" />
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3105 <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="sim_size" delta="100" />
8
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
iuc
parents: 7
diff changeset
3106 </test>
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3107 <!--test 22-->
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3108 <test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3109 <param name="region" value="chrM:10-30"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3110 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3111 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3112 <param name="track_file_style_selector" value="scale_bar_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3113 <param name="title" value="scalebar height = 5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3114 <param name="sb_where" value="right"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3115 <param name="height" value="5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3116 <param name="spacer_height" value="0.5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3117 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3118 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3119 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3120 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3121 <param name="track_file_style_selector" value="fasta_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3122 <param name="title" value="fasta from cached" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3123 <conditional name="fasta_source">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3124 <param name="fasta_source_selector" value="cached"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3125 <param name="fasta_cached" value="chrM"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3126 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3127 <param name="spacer_height" value="0.5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3128 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3129 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3130 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3131 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3132 <param name="track_file_style_selector" value="fasta_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3133 <param name="title" value="fasta from history height = 5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3134 <conditional name="fasta_source">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3135 <param name="fasta_source_selector" value="history"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3136 <param name="fasta_local" value="chrM.fa" ftype="fasta" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3137 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3138 <param name="height" value="5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3139 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3140 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3141 <param name="image_file_format" value="png" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3142 <output name="outFileName" file="master_fasta.png" ftype="png" compare="sim_size" delta="100" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3143 </test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3144 <!--test 23-->
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3145 <test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3146 <param name="region" value="chrX:3000000-3300000"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3147 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3148 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3149 <param name="track_file_style_selector" value="xaxis_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3150 <param name="xaxis_where" value="top" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3151 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3152 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3153 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3154 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3155 <param name="track_file_style_selector" value="spacer_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3156 <param name="spacer_height" value="0.05" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3157 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3158 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3159 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3160 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3161 <param name="track_file_style_selector" value="hic_matrix_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3162 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3163 <param name="title" value="classical depth=300000 with arcs" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3164 <param name="depth" value="300000" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3165 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3166 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3167 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3168 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3169 <param name="track_file_style_selector" value="link_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3170 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3171 <conditional name="color_link">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3172 <param name="color" value="red" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3173 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3174 <param name="line_width" value="5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3175 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3176 <param name="links_type" value="loops" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3177 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3178 <param name="overlay_select" value="share-y" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3179 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3180 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3181 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3182 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3183 <param name="track_file_style_selector" value="hic_matrix_square_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3184 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3185 <param name="title" value="square with arcs" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3186 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3187 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3188 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3189 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3190 <param name="track_file_style_selector" value="link_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3191 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3192 <conditional name="color_link">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3193 <param name="color" value="red" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3194 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3195 <param name="line_width" value="5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3196 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3197 <param name="links_type" value="squares" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3198 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3199 <param name="overlay_select" value="share-y" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3200 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3201 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3202 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3203 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3204 <param name="track_file_style_selector" value="hic_matrix_square_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3205 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3206 <param name="title" value="square with arcs region2=chrX:3000000-3100000" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3207 <param name="region2" value="chrX:3000000-3100000"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3208 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3209 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3210 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3211 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3212 <param name="track_file_style_selector" value="link_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3213 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3214 <conditional name="color_link">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3215 <param name="color" value="red" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3216 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3217 <param name="line_width" value="5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3218 <conditional name="display">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3219 <param name="links_type" value="squares" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3220 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3221 <param name="overlay_select" value="share-y" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3222 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3223 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3224 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3225 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3226 <param name="track_file_style_selector" value="hic_matrix_square_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3227 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3228 <param name="title" value="square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3229 <param name="region2" value="chrX:3000000-3100000"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3230 <param name="colormap" value="Blues"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3231 <param name="transform" value="no" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3232 <param name="boundaries_file" value="tad_classification.bed" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3233 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3234 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3235 <param name="image_file_format" value="png" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3236 <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="sim_size" delta="1200" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3237 </test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3238 <!--test 24-->
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3239 <test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3240 <param name="region" value="2:34704975-34705208"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3241 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3242 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3243 <param name="track_file_style_selector" value="maf_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3244 <param name="track_input_maf" value="first.maf" ftype="maf"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3245 <param name="reference" value="mm10"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3246 <param name="title" value="default" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3247 <param name="spacer_height" value="1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3248 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3249 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3250 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3251 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3252 <param name="track_file_style_selector" value="maf_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3253 <param name="track_input_maf" value="first.maf" ftype="maf"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3254 <param name="reference" value="mm10"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3255 <param name="title" value="height = 3 show sequence" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3256 <param name="height" value="3"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3257 <param name="display_ref_seq" value="true"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3258 <param name="spacer_height" value="1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3259 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3260 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3261 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3262 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3263 <param name="track_file_style_selector" value="maf_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3264 <param name="track_input_maf" value="first.maf" ftype="maf"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3265 <param name="reference" value="mm10"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3266 <param name="title" value="species_order = hg19 rn5, species_labels = Human Rat" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3267 <param name="height" value="3"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3268 <param name="species_order" value="hg19 rn5"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3269 <param name="species_labels" value="Human Rat"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3270 <param name="spacer_height" value="1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3271 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3272 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3273 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3274 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3275 <param name="track_file_style_selector" value="maf_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3276 <param name="track_input_maf" value="first.maf" ftype="maf"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3277 <param name="reference" value="mm10"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3278 <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3279 <param name="height" value="3"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3280 <param name="species_order" value="hg19"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3281 <param name="species_labels" value="Human"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3282 <param name="species_order_only" value="true"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3283 <param name="spacer_height" value="1"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3284 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3285 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3286 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3287 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3288 <param name="track_file_style_selector" value="xaxis_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3289 <param name="xaxis_where" value="bottom" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3290 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3291 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3292 <param name="image_file_format" value="png" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3293 <output name="outFileName" file="test_maf.png" ftype="png" compare="sim_size" delta="1200" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3294 </test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3295 <!--test 25-->
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3296 <test>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3297 <param name="region" value="chr2:73,800,000-75,744,000"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3298 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3299 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3300 <param name="track_file_style_selector" value="bedgraph_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3301 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3302 <param name="title" value="bedgraph color = blue" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3303 <param name="height_bedgraph" value="5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3304 <param name="color" value="blue" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3305 <param name="show_data" value="true" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3306 <param name="max_value" value="5" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3307 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3308 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3309 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3310 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3311 <param name="track_file_style_selector" value="vhighlight_track_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3312 <param name="track_input_bed_single" value="islands.bed" ftype="bed"/>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3313 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3314 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3315 <repeat name="tracks">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3316 <conditional name="track_file_style_conditional">
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3317 <param name="track_file_style_selector" value="xaxis_option" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3318 <param name="xaxis_where" value="bottom" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3319 </conditional>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3320 </repeat>
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3321 <param name="image_file_format" value="png" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3322 <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="sim_size" delta="1200" />
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3323 </test>
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3324 </tests>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3325 <help><![CDATA[
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3326
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3327 pyGenomeTracks
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3328 ==============
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3329
2
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
3330 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents: 1
diff changeset
3331 Currently, it is possible to plot:
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3332
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3333 - bigwig
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3334 - bed/gtf (many options)
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3335 - bedgraph
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3336 - epilogos
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3337 - narrow peaks
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3338 - links
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
iuc
parents: 8
diff changeset
3339 - Hi-C matrices (cool or HiCExplorer h5)
11
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3340 - Fasta
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
iuc
parents: 10
diff changeset
3341 - MAF (multiple alignment format)
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3342
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3343 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff changeset
3344
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
3345 Usage
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
3346 -----
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3347
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
3348 This tool takes various types of tracks as input:
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3349
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3350 - **Hi-C tracks:**
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3351 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3352 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3353 - **Chromatin states:** display blocks of different colors following a bed file.
9
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3354 - **Gene track / Bed Track:** display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3355 - **Link track:** display links (pair of coordinates) as arcs, triangles or loops.
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3356 - **NarrowPeak track:** display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3357 - **Bigwig track:** generic bigwig track plotting.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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diff changeset
3358 - **Bedgraph track:** generic bedgraph track plotting.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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diff changeset
3359 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
3360 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
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3361 - **Vhighlight:** vertical rectangles drawn on top of all tracks following a bed file. It is used as a visual support to highlight some regions.
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3362 - **Hlines:** horizontal lines drawn either by themselves or on top of other tracks.
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3363 - **Spacer:** Add some space between two tracks.
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2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3364 - **X-axis:** Plot x-axis scale wherever you want.
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3365 - **Scale bar track:** Plot scale bar.
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3366 - **Fasta track:** Display sequences from fasta.
7dd841a32245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def
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3367 - **Maf track:** Display alignments from maf.
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3368
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3369 For each track, parameters for the color, the width or the font size can be defined.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3370
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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diff changeset
3371 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3372
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3373 Output
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3374 ------
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3375
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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3376 Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used):
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3377
12
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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3378 .. image:: static/images/demo.png
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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3379 :width: 45 %
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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diff changeset
3380 .. image:: static/images/demo2.png
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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diff changeset
3381 :width: 45 %
14e7c35f3d00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404
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3382
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3383
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3384 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3385
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3386 | For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3387
9
2824d77cd8f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835"
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3388 .. _readthedocs: https://pygenometracks.readthedocs.io
0
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3389 .. _github: https://github.com/deeptools/pyGenomeTracks
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3390 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3391 ]]></help>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3392 <expand macro="citations" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
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3393 </tool>